Technical details
library(GeoPressureR)
library(leaflet)
library(leaflet.extras)
library(raster)
library(dplyr)
library(ggplot2)
library(kableExtra)
library(plotly)
library(GeoLocTools)
setupGeolocation()
knitr::opts_chunk$set(echo = FALSE)
load(paste0("../data/1_pressure/", params$gdl_id, "_pressure_prob.Rdata"))
load(paste0("../data/2_light/", params$gdl_id, "_light_prob.Rdata"))
load(paste0("../data/3_static/", params$gdl_id, "_static_prob.Rdata"))
load(paste0("../data/5_wind_graph/", params$gdl_id, "_wind_graph.Rdata"))
col <- rep(RColorBrewer::brewer.pal(8, "Dark2"), times = ceiling(max(pam$sta$sta_id) / 8))
All the results produced here are generated with (1) the raw geolocator data, (2) the labeled files of pressure and light and (3) the parameters listed below.
kable(gpr) %>% scroll_box(width = "100%")
| gdl_id | keep | multisensor | description | crop_start | crop_end | thr_dur | extent_N | extent_W | extent_S | extent_E | map_scale | map_max_sample | map_margin | prob_map_s | prob_map_s_calib | prob_map_thr | shift_k | kernel_adjust | calib_lon | calib_lat | calib_1_start | calib_1_end | calib_2_start | calib_2_end | calib_2_lon | calib_2_lat | prob_light_w | thr_prob_percentile | thr_gs | thr_as | low_speed_fix | ringNo | scientific_name | common_name | mass | wing_span | Color |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 24TA | TRUE | TRUE | ok | 2020-08-20 | 2021-06-10 | 0 | 0 | 34 | -16 | 42 | 10 | 300 | 40 | 0.7 | NA | 0.9 | 0 | 1.4 | 39.9889 | -3.37827 | 2020-08-20 | 2020-11-01 | 2021-05-08 | 2021-06-10 | NA | NA | 0.09 | 0.9 | 120 | 100 | 15 | NA | Cossypha natalensis | Red-capped Robin-Chat | 34.2 | 35 | #EBC344 |
The labeling of pressure data is illustrated with this figure. The black dots indicates the pressure datapoint not considered in the matching. Each stationary period is illustrated by a different colored line.
pressure_na <- pam$pressure %>%
mutate(obs = ifelse(isoutlier | sta_id == 0, NA, obs))
p <- ggplot() +
geom_line(data = pam$pressure, aes(x = date, y = obs), colour = "grey") +
# geom_point(data = subset(pam$pressure, isoutlier), aes(x = date, y = obs), colour = "black") +
# geom_line(data = pressure_na, aes(x = date, y = obs, color = factor(sta_id)), size = 0.5) +
geom_line(data = do.call("rbind", shortest_path_timeserie) %>% filter(sta_id > 0), aes(x = date, y = pressure0, col = factor(sta_id))) +
theme_bw() +
scale_colour_manual(values = col) +
scale_y_continuous(name = "Pressure(hPa)")
ggplotly(p, dynamicTicks = T) %>% layout(showlegend = F)